Download Biochemistry - Chemical Reactions of Living Cells [Vol 1] 2nd ed - D. Metzler (Elsevier, 2003) WW PDF

TitleBiochemistry - Chemical Reactions of Living Cells [Vol 1] 2nd ed - D. Metzler (Elsevier, 2003) WW
TagsMedical
LanguageEnglish
File Size27.8 MB
Total Pages940
Document Text Contents
Page 2

The Scene of Action 1

Amino Acids, Peptides, and Proteins 39

Determining Structures and Analyzing Cells 95

Sugars, Polysaccharides, and Glycoproteins 161

The Nucleic Acids 199

Thermodynamics and Biochemical Equilibria 281

How Macromolecules Associate 325

Lipids, Membranes, and Cell Coats 379

Enzymes: The Catalysts of Cells 455

An Introduction to Metabolism 505

The Regulation of Enzymatic Activity and Metabolism 535

Transferring Groups by Displacement Reactions 589

Enzymatic Addition, Elimination, Condensation,

and Isomerization: Roles for Enolate and Carbocation

Intermediates 677

Coenzymes: Nature’s Special Reagents 719

Coenzymes of Oxidation – Reduction Reactions 765

Transition Metals in Catalysis and Electron Transport 837

Chapter 1.

Chapter 2.

Chapter 3.

Chapter 4.

Chapter 5.

Chapter 6.

Chapter 7.

Chapter 8.

Chapter 9.

Chapter 10.

Chapter 11.

Chapter 12.

Chapter 13.

Chapter 14.

Chapter 15.

Chapter 16.

Table of Contents
Volume 1

Page 470

467

maintained. As can be seen from the graph, this ex-
change rate increases monotonically as substrate
concentrations are increased. This is also true for the
rate of ATP–ADP exchange. The fact that both ex-
change rates increase continuously indicates random
binding of substrates.55 The inequality of the two
maximal exchange rates suggests that release of glucose
6-phosphate may be slower than that of ADP.

Figure 9-7B shows similar plots for lactate dehydro-
genase.53 In this case, after an initial rise (that is not
regarded as significant), the pyruvate*–lactate exchange
reaches a high constant value as the amount of pyruvate
is increased (with a constant [pyruvate] / [lactate] ratio
of 1/35). However, the NAD*–NADH exchange in-
creases rapidly at first but then drops abruptly as the
pyruvate and lactate concentrations continue to in-
crease. This suggests an ordered mechanism (Eq. 9-43)
in which NAD+ and NADH represent A and Q, respec-
tively, and pyruvate and lactate represent B and P. As
the concentrations of B and P become very high, the

(9-51)

the reaction of an enzyme with two substrates A and
B with a random order of binding is depicted. (In
contrast, Eq. 9-43 shows the case of ordered binding
of two substrates.) When complex EAB is formed, it
can decompose to free enzyme and to the single prod-
uct P. Each one of the nodes, which are numbered 1– 4
in the diagram, corresponds to a single form of the
enzyme. The appropriate first-order rate constant or
apparent first-order constant is placed by each arrow.
The methods provide easy rules for deriving from
such a scheme the steady-state rate equation.

The importance of the simplified schematic methods
is apparent when one considers that the steady-state
rate equation for Eq. 9-50 would have 6 terms in the
numerator and 12 terms in the denominator.51 In the
more complex case in which EAB breaks down to two
products P and Q with a random order of release, the
rate equation contains 672 terms in the denominator.
In such cases it is worthwhile to enlist the help of a
computer in deriving the equation.24,52– 54

The rapid equilibrium assumption. Rate equa-
tions for enzymes are often simplified if a single step,
e.g., that of reaction of complex EAB to product in Eq.
9-50, is rate limiting.54a If it is assumed that all reaction
steps preceding or following the rate-limiting step are
at equilibrium, the equation for random binding with
a two-substrate and two-product reaction simplifies to
one whose form is similar to that obtained for ordered
binding (Eq. 9-44). In the absence of products P and Q
Eq. 9-44 will correctly represent the steady-state rate
equation corresponding to Eq. 9-50. However, this
simplification may not be valid for a very rapidly
acting enzyme.

Isotope exchange at equilibrium. Consider the
reaction of substrates A and B to form P and Q (Eq.
9-51). If both reactants and both products are present
with the enzyme and in the ratio found at equilibrium
no net reaction will take place. However, the reactants
and products will be continually interconverted under
the action of the enzyme. Now if a small amount of

highly labeled reactant (A* or B*) is added, the rate at
which isotope is transferred from the labeled reactant
into one or the other of the products can be measured.
In general, a label in one of the substrates will appear
in only one of the products.

Figure 9-7A shows the rate of exchange of isotopi-
cally labeled glucose (glucose*) with glucose 6-phosphate
as catalyzed by the enzyme hexokinase (Chapter 12).
The exchange rate is plotted against the concentra-
tion of glucose 6-phosphate with the ratio [glucose] /
[glucose 6-phosphate] constant at 1/19, such that an
equilibrium ratio for reactants and products is always

A + B P + Q

Figure 9-7 (A) Effect of glucose and glucose 6-phosphate
concentrations on reaction rate of yeast hexokinase at equi-
librium. Reaction mixtures contain 1– 2.2 mM ATP, and 25.6
mM ADP at pH 6.5. From Fromm et al.51 (B) Effect of lactate
and pyruvate concentrations on equilibrium reaction rates
of rabbit muscle lactate dehydrogenase. Reaction mixtures
contained 1.7 mM NAD+, and 30 – 46 µM NADH in Tris-
nitrate buffer, pH 7.9, 25°C. From Silverstein and Boyer.53

10

4

0 0.5

NAD NADH

pyruvate lactate

Lactate concentration, mol l–1

(pyruvate/lactate = 1/35)

E
q

u
il

ib
ri

u
m

r
ea

ct
io

n
r

at
e,

m
o

l
l-

1
m

in
-1

×
10

3

8

6

2

1.0

10

5

0 2 4

ATP ADP

glucose glucose 6-P

G 6-P molarity × 102, G/G 6-P = 1/19

E
q

u
il

ib
ri

u
m

r
ea

ct
io

n
r

at
e,

m
o

l
l-

1
m

in
-1

×
10

4

A. Information from Kinetics

A

B

Page 471

468 Chapter 9. Enzymes: The Catalysts of Cells

enzyme shuttles back and forth between EA and EQ,
but these two complexes rarely dissociate to give free
enzyme and A or Q. Hence, the A*–Q exchange rate
drops.

In other cases a label may be transferred from A
into P or from B into Q. Information on such exchang-
es has provided a valuable criterion of mechanism
which is considered in Chapter 12, Section B,4.

5. Kinetics of Rapid Reactions

The fastest steps in an enzymatic process cannot be
observed by conventional steady-state kinetic methods
because the latter cannot be applied to reactions with
half-times of less than about 10 s. Consequently, a
variety of methods have been developed18,56– 59a to
measure rates in the range of 1 to 1013 s–1.

Flowing substrates together. One of the first
rapid kinetic methods to be devised consists of rapidly
mixing two flowing solutions together in a special
mixing device and allowing the resulting reaction
mixture to move at a rate of several meters per second
down a straight tube. At a flow velocity of 10 m s–1 a
solution will move 1 cm in 10–3 s. Observations of the
mixture are made at a suitable distance, e.g., 1 cm, and
with various flow rates. Using spectrophotometry or
other observation techniques, the formation or disap-
pearance of a product or reactant can be followed. The
special advantage of this technique is that observation
can be made slowly. However, it may require large
amounts of precious reactant solutions, e.g., those of
purified enzymes.

In the stopped flow technique two solutions are
mixed rapidly by the flow technique during a period
of only 1– 2 (or a few) milliseconds. A ram drives the
solutions from syringes through a mixing chamber
into an observation chamber. After the flow stops
light absorption, fluorescence, conductivity, or other
property, is measured. A means of rapid observation
of changes during the reaction is essential. For example,
light absorption may be measured by a photomultiplier
with data being collected by a computer. Relaxation
times as short as a few milliseconds or less can be
observed in this way.59a,b

Observing relaxation. Kinetic measurements
over periods of tens of microseconds or less can be made
by rapidly inducing a small displacement from the
equilibrium position of a reaction (or series of reactions)
and observing the rate of return (relaxation) of the
system to equilibrium. Best known is the temperature
jump method devised by Eigen and associates. Over a
period of about 10–6 s a potential difference of ~ 100 kV
is applied across the experimental solution. A rapid
electrical discharge from a bank of condensers passes

through the solution (without any sparking) raising
the temperature 2 – 10 degrees. All the chemical equi-
libria for which ∆H ≠ 0 are perturbed. If some property,
such as the absorbance at a particular wavelength or
the conductivity of the solution, is measured, very
small relaxation times can be determined.

While it may not be intuitively obvious, if the
displacement from equilibrium is small, the rate of
return to equilibrium can always be expressed as a
first-order process (e.g., see Eq. 9-13). In the event that
there is more than one chemical reaction required to
reequilibrate the system, each reaction has its own
characteristic relaxation time. If these relaxation times
are close together, it is difficult to distinguish them;
however, they often differ by an order of magnitude
or more. Therefore, two or more relaxation times can
often be evaluated for a given solution. In favorable
circumstances these relaxation times can be related
directly to rate constants for particular steps. For
example, Eigen measured the conductivity of water
following a temperature jump18 and observed the rate
of combination of H+ and OH– for which τ at 23ºC
equals 37 x 10–6 s. From this, the rate constant for
combination of OH– and H+ (Eq. 9-52) was calculated
as follows (Eq. 9-53):

k = 1/ {τ ( [ OH–] + [ H+] )} = 1.3 x 1011 M–1 s–1

Pressure jump and electric field jump methods
have also been used, as have methods depending upon
periodic changes in some property. For example, absorp-
tion of ultrasonic sound causes a periodic change in
the pressure of the system.

Rapid photometric methods. Another useful
method has been to discharge a condenser through
a flash tube over a period of 10–12 to 10–4 s, causing a
rapid light absorption in a sample in an adjacent parallel
tube. Following the flash, changes in absorption spec-
trum or fluorescence of the sample can be followed.
The availability of intense lasers as light sources has
made it possible to follow the results of light flashes of
5– 10 picosecond duration and to measure extremely
short relaxation times (Chapter 23).58,59

Some results. Rapid kinetic methods have revealed
that enzymes often combine with substrates extremely
quickly,60 with values of k1 in Eq. 9-14 falling in the
range of 106 to 108 M–1 s–1. Helix–coil transitions of
polypeptides have relaxation times of about 10–8 s,
but renaturation of a denatured protein may be much
slower. The first detectable structural change in the
vitamin A-based chromophore of the light-operated
proton pump bacteriorhodopsin occurs in ~ 5 x 10–8 s,
while a proton is pumped through the membrane in

H+ + OH H2O


(9-53)

(9-52)

Page 939

936 Volume 1 Index

theory 483
Transketolase 733, 736
Translation of genetic information, 5. See also

Protein synthesis
definition of 5
nick 257
regulation of 536

Translocation
of proteins 519 – 521

Transmembrane proteins 391
Transmethylation 591, 592

kinetic isotope effects on 592
Transmission coefficient κ 483
Transport, See also specific substrates

of ions 420 – 425
through membranes 400 – 415
via pores and channels 401– 403

Transporters
12-helix 415 – 417
membrane 411– 427
sugar 415, 416

Transposable genetic elements (transposons)
249

Tn3 219
Transsialidase 187
Treadmilling

of microtubules 372
Trehalose 167, 168s

in fungi 168
in insects 168

Triacylglycerol 381, 382s
Trialkyl lock 495s
Trichina 24
Tricholomic acid 739
Trichonympha 19
TRICINE buffer 99

pKa value of 99
Triclosan 777s, 777
Triethanolamine buffer 99

pKa value of 99
Trigonal bipyramid 638

as transition state in pseudorotation
638

Trigonal carbon atoms 680, 681
Trigonal prochiral centers 480, 481
Triiodothyronine 572
Trimethoprim 805s

inhibition of 805
Trimethylamine dehydrogenase 782, 784s
Trimethylarsonium lactic acid, 387s
Trimethyllysine

in ubiquitin 525
Tripeptidyl peptidase 140, 610
Triose phosphate isomerase 693, 694s

barrel structure 77s
high catalytic activity 693
target for antitrypanosomal drugs 693

Triphosphopyridine nucleotide (TPN+,
NADP+) 767. See also NADP+, NADPH

TRIS buffer
pKa value of 99

Tritium
properties of 110

Triton X 403s
tRNA 230, 231, 231s, 233s

19F NMR spectrum of 270
1H NMR spectrum of 268
wobble position 231

Tropical macrocytic anemia 802
Tropoelastin 436
Tropomodulin 406
Tropomyosin 370, 406

coiled coil structure of 71
Troponin C 313, 314
Trp repressor protein 239, 240s
Truffles 20
Tryosine kinases 657
Trypanosome 19

DNA circles in 219
mitochondria of 14

Trypanothione 552
Trypanothione reductase 785
Tryparsamide 597s
Trypsin 66, 116, 609. See also Chymotrypsin

hydrogen-bonding network, structure
612

specificity 117
turnover number of 457

Trypsinogen 609, 615s
oxyanion hole, structure 615

Tryptases 610
Tryptic peptides 117
Tryptophan (Trp, W) 52s

absorption spectrum of derivative 123
Cβ-hydroxylated 853
nicotinamide activity 769

Tryptophan indole-lyase 742
quinonoid intermediate 750

Tryptophan synthase 742
Tryptophan tryptophanylquinone (TTQ)

817, 817s
T system of tubules 12
TTQ See Tryptophan tryptophanylquinone
Tuberculosis 7
Tubular myelin 386
Tubulin 370, 372s
Tumor suppressor gene 407, 574
Tungsten 893
Tunicates

vanadium in 25
Tunichlorin(s) 880s, 881
Tunneling

quantum mechanical 494, 771, 848
vibration-assisted 494

Turnover numbers of an enzyme 457
Turns

beta 78
in protein structures 72, 74

Twisted sheets 63
Two-fold (dyad) axes 134

in oligomers 337– 348
Typhoid fever

S. typhi 7
Tyrosinase 886
Tyrosine (Tyr, Y) 52s

absorption spectrum of derivative 123
iodination 126

Tyrosine decarboxylase 737
Tyrosine phenol-lyase 742
Tyrosine protein kinases (MEK) 578
Tyrosine-O-sulfate 548
Tyrosyl radical 864
Tyvelose 180s

U
Ubichromanol 818, 819s
Ubiquinones (coenzyme Q) 392, 514, 818,

819s
Ubiquitin 81, 524s

activating enzyme 524, 525

carboxyl-terminal hydrolases 525
conjugating enzymes 524
genes 525
protein ligase 524

UDP-galactose
conversion to UDP glucose 778

UDP-galactose 4-epimerase 778
Ulothrix 21
Ultracentrifugation 108, 109
Ultracentrifuge 100

analytical 108
optical system, figure 109

Ultrafiltration 100
Ultrasensitive responses 567
Ultrasonic sound 468
UMP (Uridine 5'-phosphate) 200, 200s, 203
Unimolecular processes 457
Uniporters 414
Units, International System 2
Unsatisfied ends of hydrogen bonded chains

64
Uracil (Ura, U) 199s, 203

tautomerism of 45
Urate oxidase 886
Urea 82s, 478s
Urea carboxylase 730
Urease 478, 877, 878

active site of, 877s
mechanism of 877

Ureido anion 726s
Uric acid 203s

formation of 890
Uridine (Urd) 203, 234s

absorption spectra of 205
tautomer, minor 205s

Uridine 5'- phosphate. See UMP
Uridine diphosphate glucose (UDP-Glc) 515s,

720
Uridylate kinase 655
5'-Uridylic acid. See UMP
Urocanase reaction 778
Urocanic acid 755, 756s
Urokinase 634
Uronic acid 164
Uroporphyrin(s) 843
Uroporphyrin I, 845s
Urothione 804s, 891
Urticaria 385
Usher protein 364

V
Vacuole(s) 10, 11, 12

definition of 3
Valine (Val, V) 52s

biosynthesis of 527, 712
branched fatty acids from 381

Valinomycin 414, 415s
effect on potassium transport 414

van der Waals contact surfaces
of purines and pyrimidines 207

van der Waals forces 46
van der Waals radii 40, 41
Vanadate

as inhibitor of ATPases 889
insulinlike action 889

Vanadium 856, 889
Vanadocytes 889
Vanadoproteins 889

Page 940

937Volume 1 Index

van’t Hoff equation 289
Vapor phase chromatography 103
Vascular plants 29
Vasopressin 54s, 542, 563

receptor 554
Vesicle(s), coated 426
VHL (van Hippel-Lindau cancer syndrome)

564
Vibrio 7

definition of 6
Vimentin 369
Vinblastine 371
Vincristine 371
Vinculin 406
Vinylpyridine 116s
Viral oncogenes 573
Virion 244
Viroids 247
Virus(es) 244 – 249. See also Bacteriophage

adeno 247
baculo 247
binding to cells 186
BK 247
cauliflower mosaic 247
characteristics, table 245
coat 345
DNA, table 245
dsRNA 244, 244 – 247
electron micrographs of 246
Epstein-Barr 247
hepatitis A 247
hepatitis delta 247
herpes 247
human immunodeficiency virus (HIV)

248
life cycles of 248
Mengo 247
oncogenic 248
papova 244
picorna 247
plant 346
polio 247
polyhedral structures 344
polyoma 247
pox 247
protein coat 334
rhabdo 247
rhino 247
RNA containing 247, 248

table 245
satellite tobacco mosaic 343s
satellite tobacco necrosis 247, 343s, 344
simian (SV40) 244
ssDNA 244
tobacco mosaic 247
toga 247

Virus fd protein sheath 335s
Virus φX174

assembly of virion structure 365
Vitamin(s) 719. See also Individual vitamins

deficiency diseases 721
discovery of 721

Vitamin B complex 721
nutritional requirements 756

Vitamin B1 331. See also Thiamin
Vitamin B12 721, 866 – 877. See also Cobalamin,

Cyanocobalamin
adenosyltransferase 870
blood levels 869
cobalt in 866 – 877
coenzyme forms 867
nutritional requirements 756

Vitamin B12 coenzyme 864. See also Cobalamin
dependent reactions, table 871
enzymatic functions 870 – 877
isomerization reactions 872
nonenzymatic cleavage 870
ribonucleotide reductase 871

Vitamin B6 family 721, 738
nutritional requirements 756

Vitamin C. See Ascorbic acid (ascorbate)
Vitamin D 721

deposition of calcium in bones 314
Vitamin E 721. See also Tocopherols

nutritional requirement 822
Vitamin K 721, 818, 819s, 820 – 822

in blood clotting 821
dihydro 820
epoxide 820
phylloquinone 821

Vitronectin 409
Voltage-gated K+ channel 412
Volvox 21
von Szent-Györgyi, Albert 83
von Willebrand factor 409, 633
V system 475

W
Wald, George 84
Warburg, Otto H. 83, 767
Warfarin 821, 822s
Water

addition to carbonyl 677
clusters of molecules 49
content in cells 30
content in tissues 31
diffusion constant of 461
hydrogen bonding of 48
properties of 49 – 51
structure of 49, 50

Watson -Crick structure
of DNA 200

Watson, James D. 84, 200
Watson-Crick base pair 207, 208, 231
Waxes 382, 382s
WD repeat 67
Wheat, genome 12
Whooping cough 548
Wilkins, Maurice F. 200
Wilson’s disease 883
Winding number. See DNA, circular, linking

number
Wobble pairing 209
Wood-Ljundahl pathway 881
Work 282

chemical 282
to concentrate 1 mol of a substance

283
electrical 282, 302
electrochemical 300
mechanical 282
to raise 1 kg 1 m 283
to remove two charges 47

World Wide Web
protein sequences/ structures 148

Wortmannin 566s
Wounds, healing of 29

X
X-ray diffraction 132 – 137

difference electron density map 136
electron density map 135
isomorphous replacement method 133
MAD phasing 135
refinement 136
space groups 133

X-rays
anomolous scattering 135

Xanthan gum 179
Xanthine 203s
Xanthine dehydrogenases 794, 825, 890

molybdenum in 890
Xanthine oxidase 890, 892
Xanthopterin 803, 804s
Xenobiotics 550
X-ray diffraction 611
Xylanases 602, 603
Xylans 165, 170, 175
Xylem 30
Xyloglucan 177
α-D-Xylopyranose 695s
Xylose (Xyl) 163s, 165s, 175
Xylose isomerase 527, 693, 695
D-Xylose (Xyl) 162
Xylosidases 602
Xylulose 164s

Y
Yeasts 20
Yellow fever 247
Ylid 733s

Z
Z (zusammen) configuration 43
Zinc 317, 680

in alcohol dehydrogenases 772 – 775
content of human 680

Zinc finger protein 241, 242s, 243s, 680
Zinc ion(s)

chelation by imidazole groups 625
in enzymes 773
replacements 680

Zinc proteases 625 – 627
FtsH 628

Zwitterion 41
Zygote 17
Zymogen 519, 609. See also Proenzyme;

Proenzyme(s)
Zymogen granules 609
Zyxin 406

Similer Documents